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Configuration
Stephan Reichl edited this page Sep 11, 2024
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This depends on the module and is always described in a separate README.md located in the module's config folder (i.e., {module}/config/README.md). Most often it is 1 configuration file (.yaml) for configuring the analysis (e.g., parameters) and 1-2 annotation files (.csv) describing the data or data-specific configurations (e.g., file paths or metadata).
Tip
We strongly recommend using Snakecase (e.g., snake_case) or Camelcase (e.g., camelCase) for (sample/column) names or variables to avoid R-related complications (i.e., avoid dots . or hyphens -).
Specify workflow-specific resources or command line arguments (CLI) in the workflow-profile {module}/workflow/profiles/default.config.yaml, which supersedes global Snakemake profiles.